This has been an interesting comparison. After reading on both devices I've made a final decision and am returning one of them.
The Kindle is years ahead in terms of software polish. Everything works, the interface is super slick, the store and Goodreads integration are both done to perfection. The e-ink display tuning is just right, the screen refreshes enough that ghosting is never really an issue.
The Kobo interface on the other hand has some jank. It'll display content faster than the screen can refresh, there will be ghosting, navigation is clunky.
That all being said, once you are actually reading a book instead of navigating, I prefer the Kobo. The bigger screen, seemingly more contrast-y display and seemingly better backlight make it my preferred device for actually reading books. The lack of polish in the Kobo interface doesn't matter once I get font and formatting settings dialed in and start actually reading.
So Kindle is headed back to Bezos. It is a great device and I'd recommend it without qualification, but I like the Kobo better and there is no reason to keep both.